Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015

Escherichia coli K-12 substr. MG1655 RNA: CyaR small regulatory RNA

Gene: cyaR Accession Numbers: G0-8878 (EcoCyc), b4438, ECK2078

Synonyms: ryeE

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

CyaR is a small RNA that promotes degradation of the ompX [Johansen08, De09], yqaE, nadE, and luxS mRNAs [De09]. Additional targets of CyaR have been identified by comparative genomics [Wright13]. Regulation depends on the presence of Hfq [Johansen08]. Hfq and CyaR interact [Wassarman01], and Hfq may stabilize CyaR [Johansen08].

In an hfq mutant, significantly less CyaR accumulates than in wild type [Moon11]; CyaR is also more unstable in a pnp mutant [De11].

CyaR expression is increased by cAMP-CRP and subject to catabolite repression [Johansen08, De09]; its expression is also upregulated by the alternative sigma factor of the envelope stress response, σE [Johansen08].

Ryx: "RNA of unknown function at X position (10 minute) in the genome" [Wassarman01]

CyaR: "cyclic AMP-activated RNA" [Johansen08]

Reviews: [Gottesman01, Hershberg03, Papenfort09, De10, Richards11]

Citations: [Sylwan10]

Map Position: [2,165,138 -> 2,165,224] (46.67 centisomes)
Length: 87 bp

Genetic Regulation Schematic: ?

Unification Links: ASAP:ABE-0047258 , EchoBASE:EB4522 , EcoGene:EG31153 , EcoliWiki:b4438 , PortEco:cyaR , RegulonDB:G0-8878

GO Terms:

Biological Process: GO:0070928 - regulation of mRNA stability, ncRNA-mediated Inferred from experiment [De09, Johansen08]
Molecular Function: GO:0000499 - base pairing with mRNA Inferred from experiment [De09]
GO:0005515 - protein binding Inferred from experiment [Wassarman01]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [De09]

MultiFun Terms: information transfer RNA related antisense RNA
regulation type of regulation posttranscriptional antisense RNA

Regulated Transcription Units (7 total): ?


Gene Local Context (not to scale): ?

Transcription Unit:


Ingrid Keseler on Thu Jul 24, 2008:
Gene start and end positions corrected based on [Johansen08 ].
Suzanne Paley on Thu Oct 21, 2004:
Gene boundaries added from U00096.2 release of genome

Last-Curated ? 14-Nov-2013 by Keseler I , SRI International


De09: De Lay N, Gottesman S (2009). "The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior." J Bacteriol 191(2);461-76. PMID: 18978044

De10: De la Cruz MA, Calva E (2010). "The complexities of porin genetic regulation." J Mol Microbiol Biotechnol 18(1);24-36. PMID: 20068355

De11: De Lay N, Gottesman S (2011). "Role of polynucleotide phosphorylase in sRNA function in Escherichia coli." RNA 17(6);1172-89. PMID: 21527671

Gottesman01: Gottesman S, Storz G, Rosenow C, Majdalani N, Repoila F, Wassarman KM (2001). "Small RNA regulators of translation: mechanisms of action and approaches for identifying new small RNAs." Cold Spring Harb Symp Quant Biol 66;353-62. PMID: 12762038

Hershberg03: Hershberg R, Altuvia S, Margalit H (2003). "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31(7);1813-20. PMID: 12654996

Johansen08: Johansen J, Eriksen M, Kallipolitis B, Valentin-Hansen P (2008). "Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP-CRP- and sigma(E)-Dependent CyaR-ompX Regulatory Case." J Mol Biol 383(1):1-9. PMID: 18619465

Moon11: Moon K, Gottesman S (2011). "Competition among Hfq-binding small RNAs in Escherichia coli." Mol Microbiol 82(6);1545-62. PMID: 22040174

Papenfort09: Papenfort K, Vogel J (2009). "Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level." Res Microbiol 160(4):278-87. PMID: 19366629

Richards11: Richards GR, Vanderpool CK (2011). "Molecular call and response: the physiology of bacterial small RNAs." Biochim Biophys Acta 1809(10);525-31. PMID: 21843668

Sylwan10: Sylwan L, Frumerie C, Haggard-Ljungquist E (2010). "Identification of bases required for P2 integrase core binding and recombination." Virology 404(2);240-5. PMID: 20627350

Wassarman01: Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays." Genes Dev 15(13);1637-51. PMID: 11445539

Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Mar 1, 2015, BIOCYC14B.